You can define subfigures:

\begin{pandoccrossrefsubfigures}

\begin{subfigure}{0.33\linewidth}\pandocbounded{\includegraphics[keepaspectratio,alt={1}]{fig1.png}}\caption{1\label{fig:subfig1}}\end{subfigure}%
\begin{subfigure}{0.33\linewidth}\pandocbounded{\includegraphics[keepaspectratio,alt={2}]{fig2.png}}\caption{2\label{fig:subfig2}}\end{subfigure}%
\begin{subfigure}{0.33\linewidth}\pandocbounded{\includegraphics[keepaspectratio,alt={3}]{fig3.png}}\caption{3}\end{subfigure}%

\begin{subfigure}{0.33\linewidth}\pandocbounded{\includegraphics[keepaspectratio,alt={4}]{fig4.png}}\caption{4\label{fig:subfig4}}\end{subfigure}%
\begin{subfigure}{0.33\linewidth}\pandocbounded{\includegraphics[keepaspectratio,alt={5}]{fig5.png}}\caption{5}\end{subfigure}%
\begin{subfigure}{0.33\linewidth}\pandocbounded{\includegraphics[keepaspectratio,alt={6}]{fig6.png}}\caption{6\label{fig:subfig6}}\end{subfigure}%

\begin{subfigure}{0.33\linewidth}\pandocbounded{\includegraphics[keepaspectratio,alt={7}]{fig7.png}}\caption{7\label{fig:subfig7}}\end{subfigure}%
\begin{subfigure}{0.33\linewidth}\pandocbounded{\includegraphics[keepaspectratio,alt={8}]{fig8.png}}\caption{8}\end{subfigure}%
\begin{subfigure}{0.33\linewidth}\pandocbounded{\includegraphics[keepaspectratio,alt={9}]{fig9.png}}\caption{9\label{fig:subfig9}}\end{subfigure}%

\caption{Caption}\label{fig:subfigures}

\end{pandoccrossrefsubfigures}

\begin{pandoccrossrefsubfigures}

\begin{subfigure}{1.0\linewidth}\pandocbounded{\includegraphics[keepaspectratio,alt={1}]{fig1.png}}\caption{1\label{fig:subfig21}}\end{subfigure}%

\begin{subfigure}{1.0\linewidth}\pandocbounded{\includegraphics[keepaspectratio,alt={2}]{fig2.png}}\caption{2\label{fig:subfig22}}\end{subfigure}%

\begin{subfigure}{1.0\linewidth}\pandocbounded{\includegraphics[keepaspectratio,alt={3}]{fig3.png}}\caption{3}\end{subfigure}%

\begin{subfigure}{1.0\linewidth}\pandocbounded{\includegraphics[keepaspectratio,alt={4}]{fig4.png}}\caption{4\label{fig:subfig24}}\end{subfigure}%

\begin{subfigure}{1.0\linewidth}\pandocbounded{\includegraphics[keepaspectratio,alt={5}]{fig5.png}}\caption{5}\end{subfigure}%

\begin{subfigure}{1.0\linewidth}\pandocbounded{\includegraphics[keepaspectratio,alt={6}]{fig6.png}}\caption{6\label{fig:subfig26}}\end{subfigure}%

\begin{subfigure}{1.0\linewidth}\pandocbounded{\includegraphics[keepaspectratio,alt={7}]{fig7.png}}\caption{7\label{fig:subfig27}}\end{subfigure}%

\begin{subfigure}{1.0\linewidth}\pandocbounded{\includegraphics[keepaspectratio,alt={8}]{fig8.png}}\caption{8}\end{subfigure}%

\begin{subfigure}{1.0\linewidth}\pandocbounded{\includegraphics[keepaspectratio,alt={9}]{fig9.png}}\caption{9\label{fig:subfig29}}\end{subfigure}%

\caption{Caption}\label{fig:subfigures2}

\end{pandoccrossrefsubfigures}

Figures themselves can be referenced fig.~\ref{fig:subfigures2}, as well
as individual subfigures:
figs.~\ref{fig:subfig1}, \ref{fig:subfig2}, \ref{fig:subfig29}
